He returned to his native Scotland in 1999 to become manager of Dunfermline Athletic, guiding them to the 2004 Scottish Cup Final. Calderwood left Dunfermline that summer to become manager of Aberdeen, a position he held for five seasons. Aberdeen performed relatively well in the SPL under Calderwood and reached the last 32 of the 2007–08 UEFA Cup, but suffered a number of domestic cup defeats by lower league opponents. He then had brief stints with Kilmarnock and Ross County, helping each club retain their league status. Calderwood returned to the Netherlands in March 2012, with Go Ahead Eagles.

Latterly, he spent less than a month in charge of De Graafschap in January/February 2014 before resigning.

In the summer of 2004 Willie Miller, returning to Pittodrie as Director of Football, brought Calderwood to Aberdeen to replace Steve Paterson as manager.[3] Calderwood oversaw an improvement in Aberdeen's fortunes on the playing field. They narrowly missed out on qualifying for European competition in 2004–05 and 2005–06 but finished the 2006–07 league campaign in third place, ensuring UEFA Cup qualification in 2007–08.

In December 2007, Calderwood led Aberdeen to the last 32 of European competition for the first time since 1986 with a surprising 4–0 demolition of FC Copenhagen at Pittodrie. With this great achievement, the Dons were rewarded by drawing FC Bayern Munich. Calderwood's team drew 2–2 with Bayern at Pittodrie on 14 February 2008, but Bayern pulled off a convincing 5–1 win against Calderwood's team in Germany the following week. Calderwood signed a 31⁄2-year contract to end a month of speculation about his future. Along with Calderwood, Assistant Manager Jimmy Nicholl and Coach Sandy Clark both signed similar 31⁄2-year contracts.

Calderwood took Aberdeen to that season's Scottish Cup semi final, where they lost 4–3 to Dumfries First Division side, Queen of the South. This was despite two goals and an assist from Barry Nicholson playing against his home town club.

The 2008–09 season saw Calderwood come in for some stern criticism following the club's poor start to the campaign. The Dons failed to win any of their opening four home matches, and were beaten 4–2 by Kilmarnock in the League Cup. Fans became impatient with some claiming it was time for a fresh start just as the team recovered form and with the Dons comfortably into the race for 3rd place.[4] On Sunday 18 January 2009 Calderwood led Aberdeen to a memorable victory over Celtic by 4–2 in a match that propelled Aberdeen to third in the league. However, just 3 league wins followed in the next 16 and Calderwood left the club "by mutual consent" on 24 May 2009, after the team had qualified for a place in the UEFA Europa League with a 2–1 victory over Hibernian.[5]

Calderwood was appointed manager of Kilmarnock on 14 January 2010, succeeding Jim Jefferies.[1] He agreed to a contract with the club until the end of the 2009–10 season.[1] Calderwood managed to secure Kilmarnock's SPL status for another season, but left the club in the summer after disagreeing with chairman Michael Johnston about the player and coaching budgets.[6]